PBP4 and PBP5 are involved in regulating exopolysaccharide synthesis during Escherichia coli biofilm formation

Lytic transglycosylase Slt of Pseudomonas aeruginosa as a periplasmic hub protein

Peptidoglycan is a major constituent of the bacterial cell wall. Its integrity as a polymeric edifice is critical for bacterial survival and, as such, it is a preeminent target for antibiotics. The peptidoglycan is a dynamic crosslinked polymer that undergoes constant biosynthesis and turnover. The soluble lytic transglycosylase (Slt) of Pseudomonas aeruginosa is a periplasmic enzyme involved in this dynamic turnover. Using amber-codon-suppression methodology in live bacteria, we incorporated a fluorescent chromophore into the structure of Slt. Fluorescent microscopy shows that Slt populates the length of the periplasmic space and concentrates at the sites of septation in daughter cells. This concentration persists after separation of the cells. Amber-codon-suppression methodology was also used to incorporate a photoaffinity amino acid for the capture of partner proteins. Mass-spectrometry-based proteomics identified 12 partners for Slt in vivo. These proteomics experiments were complemented with in vitro pulldown analyses. Twenty additional partners were identified. We cloned the genes and purified to homogeneity 22 identified partners. Biophysical characterization confirmed all as bona fide Slt binders. The identities of the protein partners of Slt span disparate periplasmic protein families, inclusive of several proteins known to be present in the divisome. Notable periplasmic partners (KD < 0.5 μM) include PBPs (PBP1a, KD = 0.07 μM; PBP5 = 0.4 μM); other lytic transglycosylases (SltB2, KD = 0.09 μM; RlpA, KD = 0.4 μM); a type VI secretion system effector (Tse5, KD = 0.3 μM); and a regulatory protease for alginate biosynthesis (AlgO, KD < 0.4 μM). In light of the functional breadth of its interactome, Slt is conceptualized as a hub protein within the periplasm.

Role of Penicillin-Binding Protein 1b in the Biofilm Inhibitory Efficacy of Ceftazidime Against Escherichia coli

Penicillin-binding proteins (PBPs) play an important role in bacterial biofilm formation and are the targets of β-lactam antibiotics. This study aimed to investigate the effect of the β-lactam antibiotic ceftazidime (CAZ) at subminimal inhibitory concentration (sub-MIC) on the biofilm formation of Escherichia coli by targeting PBPs. In this study, PBP1a (encoded by mrcA), PBP1b (encoded by mrcB) and PBP3 (encoded by ftsI), which have high affinity for CAZ, were deleted from the E. coli strain. The mrcB mutant showed lower adhesion, biofilm formation and swimming motility, whereas the knockout of mrcA or ftsI had no obvious influence on the biofilm-associated indicators mentioned above. After treatment with sub-MIC of CAZ, the adhesion, biofilm formation and swimming motility of the mrcB-mutant strain were not different or were slightly reduced compared with those of the untreated group. However, sub-MIC of CAZ still significantly inhibited these biofilm-associated indicators in mrcA- and ftsI-mutant strains. In addition, consistent with the bacterial motility results, the deletion of the mrcB gene reduced the flagellar numbers and the expression of flagellar structural genes, but flagellum-related indicators in the mrcB-mutant strain treated with CAZ were similar to those in the untreated group. Bioinformatic analysis showed that CAZ binds to Lys287, Lys274, Glu281, and Arg286 in PBP1b. Taken together, these results suggest that CAZ reduced flagellar synthesis and bacterial motility by binding with PBP1b and thereby inhibited the adhesion and biofilm formation of E. coli.

The RNA-Binding Protein ProQ Impacts Exopolysaccharide Biosynthesis and Second Messenger Cyclic di-GMP Signaling in the Fire Blight Pathogen Erwinia amylovora

Erwinia amylovora is a plant-pathogenic bacterium that causes fire blight disease in many economically important plants, including apples and pears. This bacterium produces three exopolysaccharides (EPSs), amylovoran, levan, and cellulose, and forms biofilms in host plant vascular tissues, which are crucial for pathogenesis. Here, we demonstrate that ProQ, a conserved bacterial RNA chaperone, was required for the virulence of E. amylovora in apple shoots and for biofilm formation in planta. In vitro experiments revealed that the deletion of proQ increased the production of amylovoran and cellulose. Prc is a putative periplasmic protease, and the prc gene is located adjacent to proQ. We found that Prc and the associated lipoprotein NlpI negatively affected amylovoran production, whereas Spr, a peptidoglycan hydrolase degraded by Prc, positively regulated amylovoran. Since the prc promoter is likely located within proQ, our data showed that proQ deletion significantly reduced the prc mRNA levels. We used a genome-wide transposon mutagenesis experiment to uncover the involvement of the bacterial second messenger c-di-GMP in ProQ-mediated cellulose production. The deletion of proQ resulted in elevated intracellular c-di-GMP levels and cellulose production, which were restored to wild-type levels by deleting genes encoding c-di-GMP biosynthesis enzymes. Moreover, ProQ positively affected the mRNA levels of genes encoding c-di-GMP-degrading phosphodiesterase enzymes via a mechanism independent of mRNA decay. In summary, our study revealed a detailed function of E. amylovora ProQ in coordinating cellulose biosynthesis and, for the first time, linked ProQ with c-di-GMP metabolism and also uncovered a role of Prc in the regulation of amylovoran production. IMPORTANCE Fire blight, caused by the bacterium Erwinia amylovora, is an important disease affecting many rosaceous plants, including apple and pear, that can lead to devastating economic losses worldwide. Similar to many xylem-invading pathogens, E. amylovora forms biofilms that rely on the production of exopolysaccharides (EPSs). In this paper, we identified the RNA-binding protein ProQ as an important virulence regulator. ProQ played a central role in controlling the production of EPSs and participated in the regulation of several conserved bacterial signal transduction pathways, including the second messenger c-di-GMP and the periplasmic protease Prc-mediated systems. Since ProQ has recently been recognized as a global posttranscriptional regulator in many bacteria, these findings provide new insights into multitiered regulatory mechanisms for the precise control of virulence factor production in bacterial pathogens.

Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies

In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.